| Solving a Generalized Distance Geometry Problem for Protein Structure Determination. | |
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MedLine Citation:
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PMID: 21424232 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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We propose a new approach to the problem of determining an ensemble of protein structures with a set of interatomic distance bounds in NMR protein modeling. Similarly to X-ray crystallography, we assume that the protein has an equilibrium structure and the atoms fluctuate around their equilibrium positions. Then, the problem can be formulated as a generalized distance geometry problem, to find the equilibrium positions and maximal possible fluctuation radii for the atoms in the protein, subject to the condition that the fluctuations should be within the given distance bounds. We describe the scientific background of the work, the motivation of the new approach and the formulation of the problem. We develop a geometric buildup algorithm for an approximate solution to the problem and present some preliminary test results as a first step concept proofing. We also discuss related theoretical and computational issues and potential impacts of this work in NMR protein modeling. |
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Authors:
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Atilla Sit; Zhijun Wu |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2011-3-18 |
Journal Detail:
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Title: Bulletin of mathematical biology Volume: - ISSN: 1522-9602 ISO Abbreviation: - Publication Date: 2011 Mar |
Date Detail:
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Created Date: 2011-3-22 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0401404 Medline TA: Bull Math Biol Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
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Department of Mathematics, Iowa State University, Ames, IA, 50011, USA, atilla@iastate.edu. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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